相关论文: Universality of Long-Range Correlations in Expansi…

We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…

Persistence in spatially extended dynamical systems (like coarsening systems and other nonequilibrium systems) is reviewed. We discuss, in particular, the spatial correlations in the persistent regions and their evolution in time in these…

In this paper, we review the literature on statistical long-range correlation in DNA sequences. We examine the current evidence for these correlations, and conclude that a mixture of many length scales (including some relatively long ones)…

Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…

Stochastic processes with renewal properties are powerful tools for modeling systems where memory effects and long-time correlations play a significant role. In this work, we study a broad class of renewal processes where a variable's value…

Collapse of the wave function appears to violate the quantum superposition principle as well as deterministic evolution. Objective collapse models propose a dynamical explanation for this phenomenon, by making a stochastic non-unitary and…

Based on a model first studied in [Physical Review A, vol. 43, 5240-5260,1991] properties of correlation function for expansion-modification systems are developed. The existence of several characteristic exponents is proved. The…

Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary…

The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…

We study the dynamics of genetic code evolution. The model of Vetsigian et al. [1] and Vetsigian [2] uses the mechanism of horizontal gene transfer to demonstrate convergence of the genetic code to a near universal solution. We reproduce…

We introduce a simple model for DNA evolution. Using the method of Peng et al.$^1$, we investigate the fractal properties of the system. For small chains and chains of intermediate size we find a fractal exponent that indicates the…

The dynamical relaxation and scaling properties of three different variants of the contact process in two spatial dimensions are analysed. Dynamical contact processes capture a variety of contagious processes such as the spreading of…

Diffusion-Limited Aggregation (DLA), the canonical model for non-equilibrium fractal growth, emerges from the simple rule of irreversible attachment by random walkers. Despite four decades of study, a unified computational framework…

It might be anticipated that there is statistical universality in the long-time classical dynamics of chaotic systems, corresponding to the universal correspondence of their quantum spectral statistics with random matrix models. We argue…

Pattern formation has been extensively studied in the context of evolving (time-dependent) domains in recent years, with domain growth implicated in ameliorating problems of pattern robustness and selection, in addition to more realistic…

We study two-component growth that mixes random deposition (RD) with a correlated growth process that occurs with probability p. We find that these composite systems are in the universality class of the correlated growth process. For RD…

Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…

Large-scale dynamical properties of complete chromosome DNA sequences of eukaryotes are considered. By the proposed deterministic models with intermittency and symbolic dynamics we describe a wide spectrum of large-scale patterns inherent…

Scale invariance and the resulting power law behaviours are seen in diverse systems. In this work we consider translation, rotational and scale invariant systems defined on a lattice, such that the variables defining the state at every…

We investigate on a possible way to connect the presence of Low-Complexity Sequences (LCS) in DNA genomes and the nonstationary properties of base correlations. Under the hypothesis that these variations signal a change in the DNA function,…